Updated Docs
Fixed doc _build location issue and rebuilt docs
Merge branch 'master' into develop
Added sphinx extention to use google analytics and modified src/docs/conf.py
removed google ananlytics script from rst since it its now included in <head> by sphinx extention
mostly a docs build
deleted the docs/_build/html directory.  I think it got created by mistake in a re-run of sphinx-quickstart
src/blacktie/utils/misc.py:
- added incomplete get_version_number() function
Changed yaml config file and scripts from using 'group_id' terminology to using 'experiment_id' and added 'replicate_id'
topic_CuffDiff_replicates: changed BaseCall.set_call_id() to use programName_conditionName_replicateID format
topic_CuffDiff_replicates: changed examples/blacktie_config_example.yaml to include condition_queue[i].replicate_id
topic_CuffDiff_replicates: src/blacktie/utils/calls.py: CuffdiffCall(): due to the bellow this should now support automatic construction of replicate bams as comma separated lists to add to the command string.
- moved get_condition_id() to self.get_condition_id() so that it can be used instead of the old -> condition['name']
- changed condition['name'] references to self.get_condition_id(condition)
- CuffdiffCall(): added uniques() and join_replicate_paths() to self.get_sample_bams() and integrated them
- CuffdiffCall(): due to the above this should now support automatic construction of replicate bams as comma separated lists to add to the command string.
# topic_CuffDiff_replicates:
## src/blacktie/utils/misc.py:
- moved uniques() from def in def to here as final home
# topic_CuffDiff_replicates
## src/blacktie/scripts/blacktie_pipeline.py
- minor refactoring to accommodate this feature
# topic_CuffDiff_replicates
## src/blacktie/utils/calls.py
- minor refactoring to accommodate this feature
# fixed issues with --mode qsub_script
Merge branch 'topic_CuffDiff_replicates' into develop
Merge branch 'develop'
Changed version number to 0.2.0rc1 in code
updated NEWS.txt